Modulome

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.9.dev0

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Modulome
        Analysis of public microbial RNA-seq data

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Contact E-mail
        avsastry@ucsd.edu
        Application Type
        Microbial RNA-seq Analysis

        Report generated on 2020-09-04, 10:46 based on data in: /home/anand/Documents/modulome/modulome-nextflow/aws_results


        General Statistics

        Showing 265/265 rows and 9/10 columns.
        Sample Name% AssignedM Assigned% AlignedM Aligned% BP Trimmed% Dups% GCLengthM Seqs
        ERX1050026
        14.0%
        1.8
        91.9%
        11.9
        5.9%
        83.1%
        55%
        97 bp
        12.9
        ERX1050027
        15.0%
        1.9
        93.5%
        12.1
        6.3%
        81.6%
        55%
        95 bp
        12.9
        ERX1050028
        51.2%
        7.7
        86.3%
        13.0
        4.6%
        74.7%
        55%
        97 bp
        15.1
        ERX1050029
        37.5%
        5.0
        70.0%
        9.3
        3.0%
        79.2%
        54%
        97 bp
        13.3
        SRX1828913
        63.0%
        11.5
        87.8%
        16.0
        3.8%
        79.2%
        54%
        98 bp
        18.2
        SRX1828914
        61.0%
        13.3
        86.7%
        18.9
        3.9%
        81.0%
        55%
        98 bp
        21.7
        SRX1828915
        59.5%
        12.0
        86.4%
        17.5
        4.4%
        80.1%
        54%
        97 bp
        20.3
        SRX1828916
        62.1%
        13.1
        88.0%
        18.5
        3.1%
        83.5%
        55%
        99 bp
        21.1
        SRX1828917
        63.2%
        12.8
        87.7%
        17.7
        3.4%
        80.4%
        55%
        98 bp
        20.2
        SRX1828918
        60.9%
        12.4
        85.8%
        17.5
        3.5%
        83.6%
        55%
        98 bp
        20.4
        SRX3158988
        10.1%
        3.4
        20.8%
        6.9
        1.2%
        77.2%
        47%
        49 bp
        33.4
        SRX3158989
        1.7%
        0.5
        4.9%
        1.5
        1.2%
        75.7%
        46%
        49 bp
        30.2
        SRX3158990
        1.3%
        0.5
        4.0%
        1.6
        1.2%
        74.5%
        46%
        49 bp
        40.2
        SRX3158991
        2.7%
        1.0
        6.6%
        2.5
        1.3%
        74.2%
        46%
        49 bp
        37.3
        SRX3158992
        5.4%
        2.0
        11.7%
        4.4
        1.3%
        77.4%
        46%
        49 bp
        37.3
        SRX3158993
        0.7%
        0.3
        2.8%
        1.0
        1.3%
        76.4%
        45%
        49 bp
        35.6
        SRX3158994
        0.6%
        0.2
        2.7%
        1.0
        1.3%
        76.6%
        46%
        49 bp
        37.0
        SRX3158995
        0.8%
        0.3
        3.0%
        1.0
        1.3%
        75.1%
        46%
        49 bp
        31.4
        SRX3158996
        6.4%
        2.3
        14.1%
        5.1
        1.3%
        79.1%
        46%
        49 bp
        36.2
        SRX3158997
        0.4%
        0.1
        2.0%
        0.7
        1.3%
        77.3%
        46%
        49 bp
        35.8
        SRX3158998
        0.5%
        0.2
        2.6%
        0.9
        1.4%
        77.8%
        46%
        49 bp
        37.0
        SRX3158999
        0.6%
        0.2
        2.6%
        0.9
        1.4%
        76.8%
        45%
        49 bp
        36.6
        SRX3159000
        13.0%
        1.4
        16.2%
        1.8
        0.7%
        81.5%
        45%
        143 bp
        10.8
        SRX3159001
        32.0%
        3.0
        39.9%
        3.8
        0.7%
        72.7%
        49%
        142 bp
        9.4
        SRX3159002
        19.1%
        2.1
        23.9%
        2.6
        0.5%
        76.3%
        47%
        143 bp
        10.9
        SRX3159003
        23.5%
        2.5
        29.8%
        3.2
        0.5%
        75.7%
        48%
        140 bp
        10.6
        SRX3159004
        19.5%
        2.1
        24.7%
        2.7
        0.4%
        79.7%
        46%
        142 bp
        11.0
        SRX3159005
        29.4%
        3.1
        36.5%
        3.9
        0.5%
        76.8%
        49%
        143 bp
        10.6
        SRX3159006
        19.6%
        2.0
        25.0%
        2.6
        0.6%
        78.6%
        47%
        141 bp
        10.2
        SRX3159007
        23.1%
        2.5
        29.0%
        3.1
        0.4%
        77.2%
        47%
        141 bp
        10.6
        SRX3159008
        17.8%
        2.0
        22.3%
        2.5
        0.5%
        75.4%
        46%
        141 bp
        11.3
        SRX3159009
        26.4%
        1.9
        33.5%
        2.4
        0.5%
        73.6%
        48%
        141 bp
        7.2
        SRX3159010
        31.5%
        2.6
        39.8%
        3.3
        0.9%
        71.8%
        50%
        131 bp
        8.3
        SRX3159011
        4.1%
        0.2
        5.5%
        0.3
        1.0%
        26.6%
        42%
        137 bp
        5.3
        SRX3159012
        24.6%
        2.3
        31.4%
        3.0
        1.0%
        60.2%
        47%
        140 bp
        9.5
        SRX3159013
        40.4%
        3.7
        52.3%
        4.8
        0.8%
        73.6%
        52%
        139 bp
        9.1
        SRX3159014
        38.9%
        3.9
        48.3%
        4.9
        0.8%
        83.9%
        51%
        138 bp
        10.2
        SRX3159015
        36.1%
        2.7
        45.4%
        3.4
        0.8%
        78.5%
        51%
        139 bp
        7.4
        SRX3159016
        30.9%
        3.1
        38.5%
        3.8
        0.8%
        78.1%
        50%
        139 bp
        10.0
        SRX3159017
        35.3%
        3.6
        44.0%
        4.5
        0.8%
        77.9%
        50%
        139 bp
        10.2
        SRX3159018
        34.9%
        3.3
        44.1%
        4.2
        0.8%
        82.4%
        51%
        138 bp
        9.4
        SRX3159019
        37.6%
        3.8
        47.2%
        4.8
        0.8%
        82.4%
        52%
        140 bp
        10.1
        SRX3159020
        33.3%
        3.8
        42.6%
        4.8
        0.8%
        80.9%
        51%
        139 bp
        11.3
        SRX3159021
        38.9%
        3.7
        50.7%
        4.8
        0.8%
        81.5%
        52%
        139 bp
        9.4
        SRX3159022
        29.6%
        2.9
        37.1%
        3.6
        0.8%
        84.1%
        50%
        140 bp
        9.8
        SRX3159023
        36.0%
        3.5
        44.7%
        4.3
        0.8%
        82.0%
        51%
        140 bp
        9.7
        SRX3159024
        31.7%
        3.4
        39.1%
        4.2
        0.8%
        79.1%
        51%
        138 bp
        10.7
        SRX3159025
        35.3%
        4.0
        44.3%
        5.0
        0.8%
        85.0%
        51%
        140 bp
        11.3
        SRX3159026
        23.8%
        1.0
        29.5%
        1.3
        0.6%
        68.7%
        49%
        138 bp
        4.2
        SRX3159027
        27.3%
        1.0
        34.5%
        1.2
        0.6%
        59.0%
        48%
        140 bp
        3.5
        SRX3159028
        22.6%
        2.1
        28.6%
        2.6
        0.7%
        74.7%
        47%
        143 bp
        9.2
        SRX3159029
        24.6%
        2.2
        30.9%
        2.8
        0.7%
        71.7%
        48%
        142 bp
        9.0
        SRX3159030
        15.9%
        1.6
        19.9%
        2.0
        0.7%
        78.7%
        45%
        143 bp
        10.0
        SRX3159031
        22.6%
        0.4
        29.3%
        0.5
        0.6%
        53.6%
        47%
        139 bp
        1.6
        SRX3159032
        4.1%
        0.4
        5.0%
        0.5
        0.9%
        58.7%
        44%
        141 bp
        10.7
        SRX3159033
        4.4%
        0.5
        6.0%
        0.6
        0.7%
        79.3%
        52%
        135 bp
        10.8
        SRX3159034
        24.4%
        2.6
        31.1%
        3.4
        0.8%
        76.2%
        53%
        133 bp
        10.8
        SRX3159035
        3.3%
        0.4
        5.1%
        0.7
        0.7%
        81.9%
        54%
        133 bp
        13.1
        SRX3159036
        16.1%
        1.8
        21.4%
        2.3
        0.8%
        70.5%
        46%
        140 bp
        10.9
        SRX3159037
        30.8%
        3.0
        40.1%
        3.9
        0.8%
        71.0%
        49%
        139 bp
        9.6
        SRX3159038
        20.2%
        0.4
        26.8%
        0.5
        0.8%
        54.4%
        48%
        138 bp
        2.1
        SRX3159039
        19.8%
        0.4
        27.0%
        0.5
        0.8%
        54.9%
        47%
        138 bp
        1.8
        SRX3159040
        19.7%
        0.4
        26.3%
        0.6
        0.7%
        55.7%
        47%
        137 bp
        2.3
        SRX3159041
        20.4%
        2.2
        27.7%
        3.0
        0.8%
        73.0%
        47%
        138 bp
        10.7
        SRX3159042
        25.5%
        3.0
        33.1%
        3.9
        0.6%
        70.7%
        49%
        140 bp
        11.9
        SRX3159043
        32.4%
        2.8
        42.9%
        3.8
        0.6%
        71.5%
        50%
        140 bp
        8.8
        SRX3159044
        27.3%
        2.6
        36.2%
        3.5
        0.6%
        70.5%
        49%
        139 bp
        9.6
        SRX3159045
        22.2%
        1.6
        29.9%
        2.1
        0.6%
        69.5%
        48%
        138 bp
        7.1
        SRX3159046
        20.2%
        1.7
        26.9%
        2.3
        0.6%
        69.5%
        47%
        139 bp
        8.4
        SRX3159047
        25.3%
        2.5
        34.4%
        3.5
        0.6%
        74.5%
        48%
        139 bp
        10.0
        SRX3159048
        21.8%
        1.6
        28.5%
        2.1
        0.7%
        71.1%
        47%
        139 bp
        7.4
        SRX3159049
        28.8%
        2.0
        36.3%
        2.5
        0.6%
        66.0%
        49%
        140 bp
        6.8
        SRX3159050
        30.0%
        2.1
        37.0%
        2.6
        0.6%
        67.7%
        49%
        140 bp
        7.0
        SRX3159051
        29.5%
        2.2
        37.5%
        2.8
        0.6%
        67.6%
        49%
        141 bp
        7.5
        SRX3159052
        19.6%
        1.5
        24.9%
        1.9
        0.6%
        71.6%
        46%
        140 bp
        7.8
        SRX3159053
        25.3%
        2.0
        32.0%
        2.5
        0.6%
        69.5%
        48%
        140 bp
        7.8
        SRX3159054
        23.8%
        1.7
        30.2%
        2.1
        0.4%
        68.1%
        48%
        141 bp
        7.1
        SRX3159055
        16.4%
        1.2
        21.3%
        1.6
        0.7%
        72.0%
        47%
        140 bp
        7.4
        SRX3159056
        15.0%
        1.1
        19.4%
        1.5
        0.7%
        66.3%
        46%
        139 bp
        7.5
        SRX3159057
        11.1%
        1.1
        14.5%
        1.4
        0.7%
        69.4%
        46%
        140 bp
        9.5
        SRX3159058
        26.1%
        2.1
        34.3%
        2.8
        0.7%
        72.3%
        48%
        139 bp
        8.1
        SRX3159059
        5.4%
        0.5
        6.9%
        0.6
        0.9%
        31.9%
        43%
        140 bp
        9.2
        SRX3159060
        16.7%
        1.3
        21.7%
        1.7
        0.7%
        71.5%
        46%
        139 bp
        7.6
        SRX3159061
        13.0%
        1.1
        17.4%
        1.5
        0.7%
        70.3%
        46%
        140 bp
        8.6
        SRX3159062
        10.6%
        1.0
        14.3%
        1.4
        0.7%
        77.1%
        45%
        139 bp
        9.8
        SRX3159063
        25.8%
        1.1
        31.7%
        1.4
        0.6%
        58.8%
        48%
        142 bp
        4.5
        SRX3159064
        2.5%
        0.2
        3.2%
        0.2
        0.7%
        64.0%
        44%
        142 bp
        6.0
        SRX3159065
        9.5%
        0.4
        11.7%
        0.4
        0.7%
        61.0%
        45%
        142 bp
        3.7
        SRX3159066
        14.2%
        1.0
        17.6%
        1.3
        0.7%
        67.1%
        46%
        141 bp
        7.2
        SRX3159067
        20.9%
        0.0
        25.6%
        0.0
        0.7%
        19.4%
        49%
        141 bp
        0.1
        SRX3159068
        2.6%
        0.2
        3.2%
        0.2
        0.7%
        63.5%
        45%
        143 bp
        6.9
        SRX3159069
        7.9%
        0.6
        9.9%
        0.7
        0.7%
        65.1%
        45%
        142 bp
        7.0
        SRX3159070
        10.8%
        0.7
        13.4%
        0.9
        0.7%
        64.7%
        45%
        142 bp
        6.5
        SRX3159071
        21.9%
        2.4
        28.5%
        3.1
        0.6%
        71.2%
        48%
        140 bp
        10.9
        SRX3159072
        2.8%
        0.2
        3.8%
        0.3
        0.7%
        70.6%
        45%
        139 bp
        8.6
        SRX3159073
        16.8%
        1.8
        21.6%
        2.3
        0.6%
        71.7%
        47%
        140 bp
        10.7
        SRX3159074
        15.4%
        1.6
        19.8%
        2.1
        0.6%
        73.8%
        47%
        140 bp
        10.6
        SRX3159075
        26.1%
        1.1
        32.5%
        1.4
        0.6%
        61.2%
        47%
        144 bp
        4.4
        SRX3159076
        20.9%
        1.9
        25.8%
        2.4
        0.6%
        74.0%
        46%
        145 bp
        9.2
        SRX3159077
        7.5%
        0.3
        9.5%
        0.4
        0.6%
        64.0%
        44%
        143 bp
        4.4
        SRX3159078
        2.9%
        0.2
        4.0%
        0.2
        0.6%
        69.9%
        43%
        143 bp
        5.3
        SRX3159079
        24.5%
        0.3
        30.8%
        0.4
        0.6%
        49.3%
        47%
        142 bp
        1.4
        SRX3159080
        25.5%
        0.9
        31.5%
        1.1
        0.6%
        60.0%
        47%
        144 bp
        3.6
        SRX3159081
        5.2%
        0.2
        7.3%
        0.3
        0.7%
        70.4%
        44%
        142 bp
        3.9
        SRX3159082
        27.3%
        3.0
        35.3%
        3.9
        0.6%
        76.7%
        49%
        140 bp
        11.0
        SRX3159083
        24.6%
        2.8
        31.6%
        3.6
        0.6%
        73.1%
        49%
        137 bp
        11.4
        SRX3159084
        7.2%
        0.8
        9.4%
        1.0
        0.7%
        67.5%
        45%
        133 bp
        10.8
        SRX3159085
        12.1%
        1.3
        17.4%
        1.9
        0.6%
        74.5%
        46%
        139 bp
        10.9
        SRX3159086
        19.4%
        0.9
        24.7%
        1.1
        0.6%
        65.2%
        47%
        141 bp
        4.4
        SRX3159087
        27.6%
        1.2
        34.4%
        1.5
        0.6%
        62.0%
        49%
        142 bp
        4.3
        SRX3159088
        28.0%
        1.4
        35.4%
        1.7
        0.6%
        66.1%
        48%
        141 bp
        4.9
        SRX3159089
        20.7%
        1.0
        25.9%
        1.3
        0.6%
        70.6%
        47%
        142 bp
        4.9
        SRX3159090
        22.1%
        0.9
        27.5%
        1.1
        0.6%
        61.0%
        48%
        141 bp
        4.0
        SRX3159091
        26.3%
        1.1
        32.6%
        1.4
        0.6%
        65.2%
        48%
        141 bp
        4.3
        SRX3159092
        17.5%
        1.2
        23.0%
        1.5
        0.7%
        67.6%
        47%
        141 bp
        6.7
        SRX3159093
        23.9%
        1.6
        31.3%
        2.1
        0.7%
        68.5%
        48%
        139 bp
        6.9
        SRX3159094
        16.9%
        1.2
        23.0%
        1.6
        0.7%
        69.1%
        47%
        140 bp
        7.0
        SRX3159095
        18.1%
        1.4
        24.4%
        1.8
        0.7%
        69.7%
        47%
        137 bp
        7.6
        SRX3159096
        21.4%
        1.3
        28.7%
        1.7
        0.7%
        70.4%
        48%
        139 bp
        6.1
        SRX3159097
        19.0%
        1.2
        25.8%
        1.6
        0.7%
        69.6%
        47%
        139 bp
        6.4
        SRX3159098
        16.2%
        1.1
        21.8%
        1.5
        0.7%
        71.8%
        47%
        140 bp
        7.0
        SRX3159099
        19.5%
        1.4
        25.2%
        1.8
        0.7%
        73.4%
        48%
        139 bp
        7.3
        SRX3159100
        38.1%
        2.7
        92.2%
        6.5
        0.6%
        82.5%
        54%
        142 bp
        7.0
        SRX3159101
        21.1%
        1.6
        60.1%
        4.6
        0.6%
        64.6%
        59%
        142 bp
        7.6
        SRX3159102
        36.7%
        2.9
        96.4%
        7.8
        0.6%
        84.6%
        54%
        142 bp
        8.0
        SRX3159103
        26.2%
        1.7
        55.7%
        3.7
        0.7%
        58.5%
        49%
        141 bp
        6.7
        SRX3159104
        12.7%
        0.3
        16.6%
        0.4
        0.7%
        65.9%
        45%
        139 bp
        2.6
        SRX3159105
        2.2%
        0.1
        2.9%
        0.1
        0.6%
        72.9%
        43%
        140 bp
        4.6
        SRX3159106
        48.5%
        1.7
        94.1%
        3.3
        0.7%
        72.6%
        54%
        141 bp
        3.5
        SRX3159107
        47.7%
        1.9
        93.0%
        3.8
        0.3%
        76.1%
        54%
        138 bp
        4.1
        SRX3159108
        17.0%
        0.7
        26.3%
        1.0
        0.9%
        26.9%
        45%
        142 bp
        3.9
        SRX3159109
        49.5%
        2.6
        84.2%
        4.4
        0.7%
        74.6%
        55%
        139 bp
        5.2
        SRX3159110
        57.2%
        2.8
        94.6%
        4.6
        0.7%
        77.2%
        55%
        139 bp
        4.9
        SRX3159111
        41.9%
        2.1
        68.6%
        3.4
        0.7%
        72.7%
        54%
        129 bp
        5.0
        SRX3159112
        55.0%
        2.6
        83.0%
        4.0
        0.7%
        78.8%
        55%
        138 bp
        4.8
        SRX3159113
        63.0%
        2.7
        94.9%
        4.1
        0.6%
        79.6%
        56%
        140 bp
        4.3
        SRX3644656
        15.4%
        18.2
        27.1%
        32.1
        0.5%
        83.9%
        54%
        75 bp
        118.4
        SRX3644657
        14.9%
        14.4
        27.5%
        26.6
        0.4%
        87.2%
        53%
        75 bp
        96.4
        SRX3644658
        17.9%
        18.4
        31.4%
        32.3
        0.5%
        87.0%
        54%
        74 bp
        102.8
        SRX3644659
        9.3%
        12.6
        17.9%
        24.3
        0.8%
        84.7%
        53%
        74 bp
        135.8
        SRX3644660
        9.8%
        11.7
        17.1%
        20.5
        0.4%
        89.0%
        53%
        75 bp
        119.6
        SRX3644661
        9.2%
        7.0
        15.8%
        12.1
        0.3%
        89.5%
        53%
        75 bp
        76.5
        SRX3644662
        17.2%
        9.1
        29.9%
        15.8
        0.5%
        81.0%
        53%
        75 bp
        53.0
        SRX3644663
        28.0%
        10.3
        46.2%
        16.9
        0.3%
        81.0%
        54%
        75 bp
        36.6
        SRX3644664
        16.3%
        8.7
        27.9%
        14.8
        0.3%
        86.8%
        54%
        75 bp
        53.1
        SRX3644665
        9.8%
        10.5
        17.8%
        19.1
        0.5%
        83.5%
        52%
        75 bp
        107.2
        SRX3644666
        12.4%
        9.6
        22.4%
        17.2
        0.4%
        87.3%
        54%
        75 bp
        76.9
        SRX3644667
        11.6%
        11.0
        21.2%
        20.2
        0.3%
        89.7%
        53%
        75 bp
        95.4
        SRX3644668
        22.1%
        12.3
        38.9%
        21.8
        0.5%
        79.7%
        54%
        74 bp
        56.0
        SRX3644669
        24.0%
        4.5
        39.8%
        7.5
        0.4%
        80.4%
        54%
        75 bp
        19.0
        SRX3644670
        32.5%
        14.6
        50.7%
        22.7
        0.3%
        82.8%
        54%
        75 bp
        44.8
        SRX3644671
        5.5%
        6.0
        12.2%
        13.3
        0.5%
        87.1%
        53%
        75 bp
        109.6
        SRX3644672
        7.5%
        5.6
        14.8%
        11.2
        0.4%
        89.1%
        53%
        75 bp
        75.2
        SRX3644673
        15.4%
        14.8
        30.2%
        29.1
        0.3%
        87.4%
        52%
        75 bp
        96.6
        SRX3644674
        48.6%
        6.7
        94.0%
        13.0
        0.6%
        64.6%
        55%
        75 bp
        13.9
        SRX3644675
        37.5%
        4.0
        96.6%
        10.4
        0.4%
        71.8%
        55%
        74 bp
        10.8
        SRX3644676
        52.9%
        9.3
        97.9%
        17.2
        0.4%
        72.6%
        56%
        75 bp
        17.6
        SRX3983989
        48.5%
        9.7
        97.0%
        19.4
        1.8%
        82.2%
        56%
        100 bp
        20.0
        SRX3983990
        58.4%
        11.0
        97.9%
        18.5
        1.3%
        80.2%
        56%
        99 bp
        18.9
        SRX3983991
        65.5%
        11.1
        94.0%
        15.9
        0.8%
        75.7%
        56%
        100 bp
        16.9
        SRX3983992
        62.7%
        11.4
        94.0%
        17.1
        1.0%
        76.1%
        56%
        100 bp
        18.2
        SRX3983993
        59.2%
        13.0
        94.7%
        20.7
        1.7%
        80.2%
        56%
        99 bp
        21.9
        SRX3983994
        28.5%
        5.7
        97.1%
        19.4
        1.2%
        87.7%
        54%
        99 bp
        20.0
        SRX3983995
        64.2%
        11.6
        93.7%
        17.0
        2.0%
        78.9%
        56%
        100 bp
        18.1
        SRX3983996
        54.7%
        11.7
        97.5%
        20.8
        1.6%
        80.8%
        56%
        99 bp
        21.3
        SRX3983997
        64.6%
        12.5
        94.2%
        18.2
        0.7%
        78.0%
        56%
        100 bp
        19.3
        SRX3983998
        56.7%
        11.9
        97.7%
        20.4
        0.8%
        81.3%
        56%
        100 bp
        20.9
        SRX3983999
        55.5%
        11.6
        93.9%
        19.7
        0.9%
        82.1%
        55%
        99 bp
        20.9
        SRX3984000
        19.3%
        4.0
        97.8%
        20.0
        0.7%
        87.9%
        54%
        99 bp
        20.5
        SRX3984001
        59.7%
        13.3
        94.5%
        21.0
        1.4%
        79.7%
        56%
        100 bp
        22.3
        SRX3984002
        21.1%
        4.3
        96.5%
        19.5
        0.7%
        89.5%
        54%
        100 bp
        20.2
        SRX3984003
        22.6%
        4.4
        89.8%
        17.4
        0.7%
        85.8%
        54%
        99 bp
        19.4
        SRX3984004
        39.8%
        8.7
        96.6%
        21.2
        0.8%
        85.2%
        55%
        99 bp
        21.9
        SRX3984005
        7.5%
        1.5
        96.3%
        19.8
        1.2%
        93.7%
        53%
        100 bp
        20.6
        SRX3984006
        52.4%
        11.8
        85.3%
        19.1
        0.8%
        74.3%
        56%
        99 bp
        22.4
        SRX3984007
        69.0%
        15.3
        96.6%
        21.4
        1.5%
        80.3%
        56%
        100 bp
        22.2
        SRX3984008
        66.1%
        14.0
        93.7%
        19.8
        1.7%
        79.4%
        57%
        100 bp
        21.1
        SRX3984009
        36.6%
        8.0
        97.8%
        21.4
        0.8%
        85.5%
        55%
        99 bp
        21.9
        SRX3984010
        48.1%
        10.7
        95.1%
        21.1
        1.7%
        83.0%
        55%
        100 bp
        22.1
        SRX3984011
        65.2%
        12.1
        97.9%
        18.2
        1.3%
        77.6%
        56%
        100 bp
        18.6
        SRX3984012
        36.4%
        6.4
        97.8%
        17.1
        0.7%
        83.9%
        55%
        100 bp
        17.5
        SRX3984013
        9.1%
        2.1
        97.5%
        23.0
        0.7%
        93.7%
        53%
        100 bp
        23.5
        SRX3984014
        59.4%
        11.8
        90.2%
        17.8
        1.0%
        79.8%
        56%
        100 bp
        19.8
        SRX3984015
        39.1%
        7.6
        89.4%
        17.3
        1.7%
        79.7%
        55%
        99 bp
        19.4
        SRX3984016
        33.2%
        6.3
        96.7%
        18.4
        1.4%
        84.7%
        54%
        99 bp
        19.1
        SRX3984017
        47.8%
        9.3
        93.4%
        18.2
        1.5%
        79.9%
        55%
        100 bp
        19.4
        SRX3984018
        73.7%
        11.5
        96.3%
        15.1
        0.7%
        76.6%
        56%
        99 bp
        15.6
        SRX3984019
        49.7%
        9.0
        97.9%
        17.7
        0.9%
        83.9%
        55%
        99 bp
        18.1
        SRX3984020
        50.3%
        9.8
        97.1%
        18.9
        0.7%
        81.9%
        55%
        99 bp
        19.5
        SRX3984021
        61.6%
        11.7
        90.0%
        17.2
        0.7%
        72.6%
        56%
        99 bp
        19.1
        SRX3984022
        17.0%
        3.7
        95.6%
        20.8
        0.8%
        89.6%
        54%
        100 bp
        21.8
        SRX3984023
        41.4%
        8.5
        98.1%
        20.2
        0.9%
        83.8%
        55%
        99 bp
        20.6
        SRX3984024
        27.5%
        7.2
        97.8%
        25.4
        1.1%
        87.5%
        54%
        99 bp
        26.0
        SRX3984025
        62.2%
        11.9
        94.0%
        18.0
        1.6%
        77.5%
        55%
        99 bp
        19.1
        SRX3984026
        3.6%
        0.8
        97.7%
        20.8
        0.6%
        95.9%
        53%
        100 bp
        21.3
        SRX3984027
        53.2%
        11.8
        97.5%
        21.6
        0.7%
        81.7%
        55%
        99 bp
        22.2
        SRX3984028
        14.7%
        3.1
        97.1%
        20.7
        1.4%
        90.5%
        54%
        99 bp
        21.3
        SRX3984029
        43.0%
        9.4
        97.5%
        21.3
        0.8%
        80.5%
        55%
        99 bp
        21.9
        SRX3984030
        49.4%
        12.5
        91.6%
        23.1
        1.3%
        79.9%
        56%
        99 bp
        25.2
        SRX3984031
        61.8%
        13.9
        91.7%
        20.7
        0.8%
        76.7%
        56%
        100 bp
        22.6
        SRX3984032
        62.9%
        11.8
        92.2%
        17.3
        1.4%
        73.7%
        56%
        99 bp
        18.8
        SRX3984033
        65.3%
        15.1
        92.8%
        21.5
        1.5%
        77.4%
        56%
        100 bp
        23.2
        SRX3984034
        70.5%
        14.2
        96.1%
        19.4
        0.9%
        81.9%
        55%
        99 bp
        20.1
        SRX3984035
        65.2%
        12.0
        81.1%
        15.0
        2.1%
        87.2%
        55%
        99 bp
        18.5
        SRX3984036
        24.8%
        5.3
        94.5%
        20.2
        0.6%
        84.7%
        54%
        99 bp
        21.4
        SRX3984037
        4.6%
        0.8
        95.8%
        17.4
        0.7%
        93.3%
        53%
        99 bp
        18.1
        SRX3984038
        6.3%
        1.4
        97.2%
        22.4
        0.7%
        95.0%
        53%
        100 bp
        23.0
        SRX3984039
        59.6%
        13.9
        89.3%
        20.9
        0.8%
        72.5%
        57%
        100 bp
        23.4
        SRX3984040
        60.1%
        10.5
        96.7%
        16.8
        1.1%
        78.3%
        56%
        99 bp
        17.4
        SRX3984041
        63.7%
        13.8
        93.8%
        20.3
        0.7%
        76.2%
        56%
        100 bp
        21.7
        SRX3984042
        25.3%
        5.1
        97.5%
        19.6
        1.2%
        88.8%
        54%
        99 bp
        20.1
        SRX3984043
        59.4%
        9.6
        98.3%
        15.8
        0.8%
        83.5%
        55%
        99 bp
        16.1
        SRX3984044
        66.1%
        11.9
        97.5%
        17.6
        0.9%
        74.0%
        56%
        100 bp
        18.0
        SRX3984045
        3.5%
        0.9
        96.7%
        24.0
        1.4%
        95.3%
        53%
        99 bp
        24.8
        SRX3984046
        57.7%
        10.4
        98.3%
        17.7
        1.3%
        80.5%
        55%
        99 bp
        18.0
        SRX3984047
        56.7%
        13.1
        89.8%
        20.8
        0.8%
        78.8%
        56%
        99 bp
        23.2
        SRX3984048
        54.0%
        11.6
        93.3%
        20.1
        1.8%
        77.2%
        56%
        100 bp
        21.5
        SRX3984049
        15.4%
        3.3
        96.1%
        20.3
        1.1%
        90.6%
        53%
        99 bp
        21.1
        SRX3984050
        10.9%
        2.6
        95.3%
        22.7
        0.7%
        92.0%
        53%
        99 bp
        23.8
        SRX3984051
        33.3%
        6.7
        93.5%
        18.8
        1.4%
        84.1%
        55%
        100 bp
        20.1
        SRX3984052
        11.3%
        2.6
        96.4%
        21.9
        1.8%
        91.7%
        54%
        99 bp
        22.7
        SRX3984053
        3.3%
        0.6
        96.1%
        18.4
        0.7%
        95.6%
        53%
        100 bp
        19.2
        SRX3984054
        52.3%
        10.4
        97.3%
        19.4
        0.8%
        78.5%
        56%
        100 bp
        20.0
        SRX3984055
        63.3%
        11.3
        94.2%
        16.8
        0.9%
        76.7%
        56%
        100 bp
        17.9
        SRX3984056
        55.9%
        13.2
        93.8%
        22.2
        1.5%
        80.7%
        56%
        100 bp
        23.7
        SRX3984057
        15.1%
        3.1
        96.0%
        19.6
        1.0%
        90.2%
        53%
        99 bp
        20.4
        SRX3984058
        44.2%
        10.0
        94.7%
        21.5
        0.7%
        84.3%
        55%
        100 bp
        22.7
        SRX3984059
        42.9%
        10.1
        96.5%
        22.8
        0.7%
        85.0%
        55%
        99 bp
        23.6
        SRX3984060
        68.4%
        14.1
        95.5%
        19.7
        0.8%
        78.7%
        56%
        99 bp
        20.7
        SRX3984061
        30.5%
        7.4
        97.7%
        23.8
        0.7%
        87.5%
        54%
        100 bp
        24.3
        SRX3984062
        57.9%
        13.8
        89.8%
        21.4
        0.8%
        82.8%
        55%
        99 bp
        23.8
        SRX3984063
        56.6%
        11.5
        96.2%
        19.5
        1.6%
        81.4%
        55%
        99 bp
        20.3
        SRX3984064
        44.6%
        8.2
        97.3%
        18.0
        1.8%
        83.0%
        55%
        99 bp
        18.5
        SRX3984065
        67.7%
        13.4
        95.4%
        18.9
        1.0%
        79.2%
        56%
        99 bp
        19.8
        SRX3984066
        53.0%
        10.2
        97.4%
        18.8
        1.2%
        81.9%
        55%
        99 bp
        19.3
        SRX3984067
        39.6%
        10.0
        97.6%
        24.7
        1.6%
        85.7%
        55%
        99 bp
        25.3
        SRX3984068
        36.1%
        7.5
        98.0%
        20.4
        0.8%
        85.4%
        54%
        99 bp
        20.8
        SRX3984069
        71.6%
        15.3
        94.2%
        20.1
        1.5%
        77.9%
        56%
        99 bp
        21.4
        SRX3984070
        40.8%
        8.7
        94.8%
        20.2
        1.4%
        81.5%
        55%
        100 bp
        21.3
        SRX3984071
        66.3%
        14.0
        93.9%
        19.8
        0.7%
        77.8%
        56%
        100 bp
        21.1
        SRX3984072
        11.1%
        2.6
        96.6%
        22.6
        1.4%
        92.2%
        53%
        100 bp
        23.4
        SRX3984073
        42.5%
        8.4
        96.8%
        19.0
        1.9%
        82.6%
        55%
        100 bp
        19.6
        SRX3984074
        60.9%
        11.0
        93.8%
        16.9
        0.9%
        79.2%
        55%
        99 bp
        18.0
        SRX3984075
        52.1%
        9.9
        85.0%
        16.2
        1.5%
        73.7%
        57%
        99 bp
        19.0
        SRX3984076
        74.7%
        12.6
        97.5%
        16.5
        1.4%
        71.8%
        56%
        99 bp
        16.9
        SRX3984077
        59.3%
        8.4
        84.2%
        12.0
        3.8%
        81.2%
        55%
        99 bp
        14.2
        SRX3984078
        55.2%
        9.5
        98.0%
        16.8
        0.9%
        79.4%
        56%
        99 bp
        17.2
        SRX3984079
        68.6%
        13.1
        94.8%
        18.1
        1.3%
        72.9%
        57%
        99 bp
        19.1
        SRX3984080
        73.4%
        14.0
        98.2%
        18.8
        1.0%
        81.6%
        56%
        99 bp
        19.1
        SRX3984081
        72.0%
        14.8
        96.7%
        19.8
        1.6%
        79.5%
        56%
        99 bp
        20.5
        SRX3984082
        39.4%
        8.6
        97.5%
        21.4
        0.7%
        84.6%
        55%
        99 bp
        21.9
        SRX3984083
        30.8%
        7.5
        92.7%
        22.7
        1.0%
        83.6%
        55%
        99 bp
        24.5
        SRX3984084
        38.3%
        6.8
        93.4%
        16.5
        1.4%
        82.6%
        55%
        100 bp
        17.6
        SRX6997962
        4.5%
        0.5
        6.3%
        0.7
        1.1%
        58.9%
        47%
        141 bp
        10.4
        SRX6997963
        42.7%
        4.1
        60.8%
        5.8
        1.0%
        74.4%
        52%
        141 bp
        9.5
        SRX6997964
        48.3%
        4.9
        65.8%
        6.7
        1.1%
        76.2%
        53%
        141 bp
        10.1
        SRX6997965
        51.1%
        4.6
        70.1%
        6.3
        1.1%
        71.3%
        54%
        138 bp
        9.0
        SRX6997966
        2.5%
        0.3
        3.7%
        0.4
        1.2%
        83.0%
        45%
        141 bp
        10.1
        SRX6997967
        29.3%
        2.7
        42.0%
        3.9
        1.1%
        78.2%
        50%
        138 bp
        9.3
        SRX6997968
        27.8%
        2.5
        37.6%
        3.4
        1.2%
        65.5%
        50%
        140 bp
        9.0
        SRX6997969
        56.2%
        6.2
        75.5%
        8.3
        1.0%
        76.5%
        54%
        140 bp
        11.0
        SRX6997970
        1.8%
        0.1
        2.6%
        0.2
        1.4%
        75.8%
        45%
        138 bp
        7.7
        SRX6997971
        16.5%
        1.8
        23.0%
        2.5
        1.4%
        64.5%
        49%
        136 bp
        11.0
        SRX6997972
        9.4%
        1.0
        12.9%
        1.4
        1.5%
        62.6%
        46%
        135 bp
        10.9
        SRX6997973
        50.6%
        5.8
        67.0%
        7.7
        1.0%
        76.7%
        53%
        141 bp
        11.6

        featureCounts

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Bowtie 1

        Bowtie 1 is an ultrafast, memory-efficient short read aligner.

        This plot shows the number of reads aligning to the reference in different ways.

        There are 3 possible types of alignment: * Aligned: Read has only one occurence in the reference genome. * Multimapped: Read has multiple occurence. * Not aligned: Read has no occurence.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        RSeQC

        RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

        Infer experiment

        Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Trimmed Sequence Lengths

        This plot shows the number of reads with certain lengths of adapter trimmed.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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